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sc-PDB

An Annotated Database of Druggable Binding Sites from the Protein DataBank

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Protein Data Bank Entry:

1hwj

2.260 Å

X-ray

2001-01-09

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:3-hydroxy-3-methylglutaryl-coenzyme A reductase
ID:HMDH_HUMAN
AC:P04035
Organism:Homo sapiens
Reign:Eukaryota
TaxID:9606
EC Number:1.1.1.34


Chains:

Chain Name:Percentage of Residues
within binding site
B100 %


Ligand binding site composition:

B-Factor:59.826
Number of residues:24
Including
Standard Amino Acids: 23
Non Standard Amino Acids: 0
Water Molecules: 1
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
0.781928.125

% Hydrophobic% Polar
40.3659.64
According to VolSite

Ligand :
1hwj_7 Structure
HET Code: ADP
Formula: C10H12N5O10P2
Molecular weight: 424.177 g/mol
DrugBank ID: -
Buried Surface Area:43.56 %
Polar Surface area: 260.7 Å2
Number of
H-Bond Acceptors: 14
H-Bond Donors: 3
Rings: 3
Aromatic rings: 2
Anionic atoms: 3
Cationic atoms: 0
Rule of Five Violation: 1
Rotatable Bonds: 6

Mass center Coordinates

XYZ
19.3573-8.82815-17.9316


Binding mode :
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Binding mode
BioSolveIT Image generated by PoseView
Protein
Binding Site
Ligand
Interaction pattern
hydrophobic (CA)
aromatic (CZ)
hydrogen bond acceptor (O)
hydrogen bond acceptor/donor (OG)
hydrogen bond donor (N)
positively ionized (NZ)
negatively ionized (OD1)
metal (ZN)

Legend:

Represent the protein/ligand binding mode, centered on the ligand
Dashed lines represents hydrogen bonds and metal interactions
Green residue labels for amino acids with hydrophobic contacts (green lines) to the ligand

Image generated using PoseView by BioSolveIT
BioSolveIT


LigandProteinInteraction
AtomAtomResidueDistance
(Å)
Angle (°)Type
N6OD2ASP- 6533.44143.44H-Bond
(Ligand Donor)
N1NASP- 6532.76157.63H-Bond
(Protein Donor)
C5'CBALA- 6543.570Hydrophobic
O1BNGLY- 6562.86146.74H-Bond
(Protein Donor)
O2BNASN- 6583.1167.14H-Bond
(Protein Donor)
C5'CEMET- 6594.330Hydrophobic
C3'CEMET- 6593.570Hydrophobic
C5'CG1VAL- 8054.480Hydrophobic
O3BOHOH- 11773.11161.71H-Bond
(Protein Donor)